|
| Status |
Public on Jan 23, 2020 |
| Title |
KSHV (+) tumors [DS013accepted_hitsmouse] |
| Sample type |
SRA |
| |
|
| Source name |
KSHV (+) tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue/cell type: KSHV-positive mECK36 tumors
|
| Growth protocol |
mECK36 cells KSHV (+) were obtained and cultured as previously described (Mutlu et al., 2007). mECK36 KSHV (+) tumors were obteined as previously described (Mutlu et al., 2007). KSHV (-) tumor cells were obtained from mECK36 tumor explants after Bac36 episome loss achieved by growth without hygromycin selection as previously described (Mutlu et al., 2007). KSHV (-) tumors were obteined by subcutaneous injection of KSHV (-) tumor cells in nude mice as previously described (Ma et a., 2013).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated and purified using the RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
mRNA from cell lines and tumor samples were processed for directional mRNA-seq library construction using the Preparation Kit according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DS013accepted
|
| Data processing |
We performed 76 nt paired-end sequencing using an Illumina NextSeq500 platform.
Illumina Casava software was used for basecalling.
The short-read sequences were mapped to the mouse reference genome (GRCm38.82) by the splice junction aligner TopHat V2.1.0.
The number of reads mapped to each gene based on the TxDb. Mmusculus gene ensembls were counted, reported and annotated using the Rsamtools, GenomicFeatures, GenomicAlignments packages.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Tab-delimited text files include log2 count per million values for each Sample
|
| |
|
| Submission date |
Jan 22, 2020 |
| Last update date |
Jan 25, 2020 |
| Contact name |
Martin Carlos Abba |
| E-mail(s) |
mcabba@gmail.com
|
| Phone |
054-221-4236711
|
| Organization name |
School of Medical Sciences - UNLP
|
| Lab |
CINIBA
|
| Street address |
60 y 120
|
| City |
La Plata |
| State/province |
Buenos Aires |
| ZIP/Postal code |
1900 |
| Country |
Argentina |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE144101 |
High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis. [RNA-Seq] |
| GSE148742 |
High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis. |
|
| Relations |
| BioSample |
SAMN13906972 |
| SRA |
SRX7620799 |
